Origin IGS: aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatatatctccttaaaaatgtgaagtgatcttactttgtataataccctaaaatataagaaaagtctatcgatataaaggcttgttttttaataatttttagattataattgaacttgccgattttatgtaaacaaaggaaatatgataaacagctcgggagaaattt Mask Tandem Repeat Region ================================================ aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Find is-nt database================================================ Query_seq: TDE0932:TDE0933|TDE0932:TDE0933:adenylate/guanylate cyclase catalytic domain protein:acetate kinase:<-->:958035..958202 168 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0932:TDE0933|TDE0932:TDE0933:adenylate/guanylate cyclase catalytic domain protein:acetate kinase:<-->:958035..958202 168 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0932:TDE0933|TDE0932:TDE0933:adenylate/guanylate cyclase catalytic domain protein:acetate kinase:<-->:958035..958202 168 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 46 End: 135 ............................................. M G K F N Y N L K I I K K Q A F I S I D F S Y I L G Y Y T K ................................. aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 59 End: 88 ..........................................................CTTGTTTTTTAATAATTTTTAGATTATAAT................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 100 End: 129 ...................................................................................................ATAGACTTTTCTTATATTTTAGGGTATTAT....................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 18 End: 47 .................TTTATCATATTTCCTTTGTTTACATAAAAT......................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 37 End: 66 ....................................TTACATAAAATCGGCAAGTTCAATTATAAT...................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0932:TDE0933|TDE0932:TDE0933:adenylate/guanylate cyclase catalytic domain protein:acetate kinase:<-->:958035..958202 168 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_002967_TDE0932_TDE0933|adenylate/guanylate cyclase catalytic domain protein:acetate kinase|NEGATIVE:POSITIVE|[958035,958202]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata aaatttctcccgagctgtttatcatatttcctttgtttacataaaatcggcaagttcaattataatctaaaaattattaaaaaacaagcctttatatcgatagacttttcttatattttagggtattatacaaagtaagatcacttcacatttttaaggagatatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUCUCCCGAGCUGUUUAUCAUAUUUCCUUUGUUUACAUAAAAUCGGCAAGUUCAAUUAUAAUCUAAAAAUUAUUAAAAAACAAGCCUUUAUAUCGAUAGACUUUUCUUAUAUUUUAGGGUAUUAUACAAAGUAAGAUCACUUCACAUUUUUAAGGAGAUAUAUA .....(((((.(((..(((((((........(((((....)))))...(((..(((.....(((((......))))).....)))..)))........)))))))..)))...........(((.((((.....)))).)))...............)))))...... (-23.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUAUCUCCUUAAAAAUGUGAAGUGAUCUUACUUUGUAUAAUACCCUAAAAUAUAAGAAAAGUCUAUCGAUAUAAAGGCUUGUUUUUUAAUAAUUUUUAGAUUAUAAUUGAACUUGCCGAUUUUAUGUAAACAAAGGAAAUAUGAUAAACAGCUCGGGAGAAAUUU ......((((((.....(((..(((((....)))))..))).....(((...((((((((...(((....))).....(((..((((..(.((((((....)))))).)..))))..)))..))))))))......)))..................))))))..... (-31.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 780 60 11 151 102 NC_002967:TDE0932|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_957944..958174_NEGATIVE 401 32 2 149 119 NC_002967:TDE1325|5end_hypothetical_protein_1361721..1361951_NEGATIVE 381 50 2 149 107 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 373 32 2 98 68 NC_002967:TDE0692|5end_hypothetical_protein_729712..729942_POSITIVE 369 32 2 198 168 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 369 32 2 199 169 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 369 32 2 98 68 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 361 32 2 74 44 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 355 40 1 214 172 NC_002967:TDE0870|5end_phosphatase/nucleotidase_892698..892928_POSITIVE 350 31 2 188 159 NC_002967:TDE0466|5end_hypothetical_protein_518854..519084_NEGATIVE 349 41 2 168 128 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 333 52 11 184 136 NC_002967:TDE1739|5end_femAB_family_protein_1791513..1791743_POSITIVE 319 33 10 99 76 NC_002967:TDE2019|5end_hypothetical_protein_2040719..2040949_NEGATIVE 319 33 10 120 97 NC_002967:TDE1694|5end_hypothetical_protein_1749366..1749596_NEGATIVE 310 39 2 160 125 NC_002967:TDE1210|5end_ATP-dependent_protease_peptidase_subunit_1243329..1243559_POSITIVE 301 32 2 186 156 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 299 31 3 190 161 NC_002967:TDE1298|5end_cyclic_nucleotide_binding_domain_protein_1335315..1335545_NEGATIVE 294 32 2 187 157 NC_002967:TDE1236|5end_triosephosphate_isomerase_1269486..1269716_POSITIVE 294 32 2 77 47 NC_002967:TDE1235|5end_hypothetical_protein_1269376..1269606_POSITIVE 289 32 2 176 146 NC_002967:TDE2394|5end_hypothetical_protein_2422612..2422842_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 32 2 81 51 NC_002967:TDE1327|3end_hypothetical_protein_1361789..1361939_NEGATIVE 381 50 2 73 31 NC_002967:TDE1333|3end_hflC_protein,_putative_1370148..1370298_POSITIVE 378 33 2 82 51 NC_002967:TDE1901|3end_ABC_transporter,_ATP-binding_protein_1922319..1922469_POSITIVE 373 32 2 34 4 NC_002967:TDE0691|3end_ABC_transporter,_ATP-binding/permease_protein_729728..729878_POSITIVE 370 32 2 81 51 NC_002967:TDE0642|3end_hypothetical_protein_678460..678610_NEGATIVE 369 32 2 87 57 NC_002967:TDE2498|3end_metallo-beta-lactamase_family_protein_2522194..2522344_NEGATIVE 369 32 2 78 48 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 361 32 2 59 29 NC_002967:TDE1973|3end_CvpA_family_protein_1987239..1987389_NEGATIVE 355 40 1 98 56 NC_002967:TDE0869|3end_hypothetical_protein_892662..892812_POSITIVE 350 31 2 36 7 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 349 41 2 95 55 NC_002967:TDE2132|3end_cobalt_ABC_transporter,_ATP-binding_protein,_putative_2162756..2162906_NEGATIVE 341 32 2 84 54 NC_002967:TDE1916|3end_glycerol_kinase_1933277..1933427_NEGATIVE 333 52 11 118 70 NC_002967:TDE1738|3end_M23/M37_peptidase_domain_protein_1791527..1791677_POSITIVE 331 34 2 90 58 NC_002967:TDE0065|3end_hypothetical_protein_72822..72972_NEGATIVE 326 43 2 103 61 NC_002967:TDE0743|3end_thioredoxin_reductase_779751..779901_POSITIVE 321 47 2 81 40 NC_002967:TDE2396|3end_putative_inner_membrane_protein_translocase_component_YidC_2423650..2423800_NEGATIVE 319 33 10 84 61 NC_002967:TDE2020|3end_YD_repeat_protein_2040734..2040884_NEGATIVE 317 39 2 97 61 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 310 39 2 93 58 NC_002967:TDE1209|3end_site-specific_recombinase,_phage_integrase_family_1243342..1243492_POSITIVE 301 32 2 82 52 NC_002967:TDE1850|3end_ABC_transporter,_permease_protein,_putative_1878227..1878377_NEGATIVE